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Strain identifier

BacDive ID: 7445

Type strain: Yes

Species: Microbacterium binotii

Strain history: CIP 101303 <-- Lab. Ident. Inst. Pasteur, Paris, France; 18.76 <-- Foch Hosp., Suresnes, France.

NCBI tax ID(s): 462710 (species)

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General

@ref: 7945

BacDive-ID: 7445

DSM-Number: 19164

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Microbacterium binotii DSM 19164 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from human blood.

NCBI tax id

  • NCBI tax id: 462710
  • Matching level: species

strain history

doi: 10.13145/bacdive7445.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium binotii
  • full scientific name: Microbacterium binotii Clermont et al. 2009

@ref: 7945

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium binotii

full scientific name: Microbacterium binotii Clermont et al. 2009

type strain: yes

Morphology

cell morphology

  • @ref: 28983
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18329Lemon yellow (1012)10-14 daysISP 3
18329Lemon yellow (1012)10-14 daysISP 4
1832910-14 daysISP 5
18329Lemon yellow (1012)10-14 daysISP 6
18329Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18329noISP 3
18329noISP 4
18329noISP 5
18329noISP 6
18329noISP 7

pigmentation

  • @ref: 28983
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7945TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18329ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18329ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18329ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18329ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18329ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
34596MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)

culture temp

@refgrowthtypetemperaturerange
7945positivegrowth28mesophilic
18329positiveoptimum28mesophilic
28983positivegrowth15-37
28983positiveoptimum30mesophilic
34596positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 28983
  • oxygen tolerance: aerobe

spore formation

  • @ref: 28983
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
28983NaClpositivegrowth0-6 %
28983NaClpositiveoptimum3 %

murein

  • @ref: 7945
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

@refobservation
28983aggregates in clumps
67770quinones: MK-10, MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2898322599arabinose+carbon source
2898317057cellobiose+carbon source
2898328757fructose+carbon source
2898328260galactose+carbon source
2898324265gluconate+carbon source
2898317234glucose+carbon source
2898317754glycerol+carbon source
2898317716lactose+carbon source
2898317306maltose+carbon source
2898329864mannitol+carbon source
2898337684mannose+carbon source
2898317814salicin+carbon source
2898317992sucrose+carbon source
2898327082trehalose+carbon source
2898318222xylose+carbon source
289834853esculin+hydrolysis
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose+fermentation
6837917306maltose+fermentation
6837916899D-mannitol+fermentation
6837965327D-xylose+fermentation
6837916988D-ribose-fermentation
6837917634D-glucose+fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis
6837917632nitrate+reduction

enzymes

@refvalueactivityec
28983acid phosphatase+3.1.3.2
28983alpha-galactosidase+3.2.1.22
28983catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18329++---++++--+-++++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18329-+++++-+-++++++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7945human bloodSuresnes, Foch hospitalFranceFRAEurope
67770Human bloodSuresnesFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood

Safety information

risk assessment

  • @ref: 7945
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7945
  • description: Microbacterium binotii strain CIP 101303 16S ribosomal RNA gene, partial sequence
  • accession: EF567306
  • length: 1406
  • database: ena
  • NCBI tax ID: 462710

GC content

@refGC-contentmethod
794571.7high performance liquid chromatography (HPLC)
2898371

External links

@ref: 7945

culture collection no.: DSM 19164, CIP 101303, NBRC 110787, JCM 16365

straininfo link

@refpassport
20218http://www.straininfo.net/strains/842154
20218http://www.straininfo.net/strains/150242

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406785Microbacterium binotii sp. nov., isolated from human blood.Clermont D, Diard S, Bouchier C, Vivier C, Bimet F, Motreff L, Welker M, Kallow W, Bizet CInt J Syst Evol Microbiol10.1099/ijs.0.003160-02009Actinomycetales/chemistry/*classification/genetics/isolation & purification, Actinomycetales Infections/*microbiology, Bacterial Typing Techniques, Base Composition, Blood/*microbiology, DNA, Bacterial/analysis/genetics, Genes, rRNA, Genotype, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Phylogeny22447697Microbacterium neimengense sp. nov., isolated from the rhizosphere of maize.Gao M, Wang M, Zhang YC, Zou XL, Xie LQ, Hu HY, Xu J, Gao JL, Sun JGInt J Syst Evol Microbiol10.1099/ijs.0.038166-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis, Zea mays/*microbiologyGenetics
Phylogeny23264499Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil.Mondani L, Piette L, Christen R, Bachar D, Berthomieu C, Chapon VInt J Syst Evol Microbiol10.1099/ijs.0.048454-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, France, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, *Uranium, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7945Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19164)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19164
18329Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19164.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2541610.1099/ijs.0.003160-019406785
28983Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125416
34596Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12863
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym